We aimed to evaluate in vivo bone response and in vitro apatite formation to titanium (Ti) implants, coated with double-stranded DNA (DNA-d) or single-stranded DNA (DNA-s), and to compare the influence in different structure of DNA, double strand and single strand on bone response and apatite formation. The bone responses to multilayered DNA-d/protamine or DNA-s/protamine coating implants were evaluated after implantation into the extracted sockets of rat maxillary molars. Apatite formation on either coating surface after immersion in simulated body fluid (SBF) was evaluated using the quartz crystal microbalance (QCM) method. DNA-d/protamine and DNA-s/protamine coatings produced more roughened and hydrophilic surfaces than untreated Ti. Animal experiments showed that higher bone-to-implant ratios were achieved 3 and 6 weeks after implantation using DNA-d/protamine and DNA-s/protamine coatings compared with Ti. QCM measurements revealed that each coating contributed to significant earlier apatite formation in SBF. We conclude that both DNA-d/protamine and DNA-s/protamine coatings enhanced early bone formation. We suggest that a DNA-multilayer coating is useful for the surface modification of a Ti implant.